(same as PM response to cakiran)
calibre doesn't really have any useful way to automate work flow or call plugins from CLI.
epubsplit did have a CLI at one time, but I removed it due to lack of interest and it's general clunkiness/incompleteness at the time.
I've re-introduced that basic CLI and polished it a bit. You'll need epubmerge.py and BeautifulSoup.py from the
source repository and a working Python 2.7.
Hope that helps.
Jim